] Re: [ccp4bb] Modeling ATP/ADP
Tried the homologues thing. There are homologues and I've done the fitting, but
this is what I consider to be subjective. I'm certain the referee will ask:
Given the quality of density for the nucleotide, how certain are the authors
that a different
... and don’t forget the Mg++ ion
Sent from my iPad
> On 23 Jul 2020, at 20:10, LMB wrote:
>
> One way of approaching such modelling uncertainties is to build explicitly a
> number of likely models, refine them and examine the difference maps
> carefully to see whether you can convince your
One way of approaching such modelling uncertainties is to build explicitly a
number of likely models, refine them and examine the difference maps carefully
to see whether you can convince yourself that one model is clearly better than
the others. At least then you will know whether the alternati
Dear Reza,
I would back Jon’s idea of looking at homologues, although
this does depend on how close the homologue is. For example, if your protein
has a “P” loop, with the Walker A sequence motif, then I think it would be very
surprising if the nucleotide bound in different wa
Tried the homologues thing. There are homologues and I've done the fitting, but
this is what I consider to be subjective. I'm certain the referee will ask:
Given the quality of density for the nucleotide, how certain are the authors
that a different fit is not possible? Have other fit poses been
